The major goals of this project are to discover and validate patterns of protein expression associated with clinically relevant tumor behaviors. These signature proteins and expression patterns may then define early detection biomarker candidates, predictors of tumor behavior, or identify potential new therapeutic targets. Proteomics has many theoretical advantages over the more established genomic and transcriptomic approaches to these questions, but has been hampered by a number of technical problems in standardization, statistical analysis, and translation to the clinic that are being rigorously identified and overcome. The Vanderbilt Lung SPORE has emerged as a leader in the field of lung cancer proteomics through progress made in the initial funding period, and now, we are applying the technology we have developed to clinical lung cancer problems, and developing the technology to probe deeper into the human proteome. In this project, we propose to build on our experience with tissue and serum-based proteomic analysis to discover new candidate biomarkers of tumor progression in a cohort of high risk individuals who develop lung cancer, of response to therapy and to explore new technological advances to improve our protein discovery and identification efforts. We will identify proteomic determinants of tumor progression in the airways of patients with preinvasive bronchial biopsies in a nested case control study of lung cancer from a unique cohort of high-risk individuals with chronic lung disease in collaboration with the Colorado Lung SPORE. We will prospectively validate and identify serum proteins from our proteomic profile predictive of response to EGFrTKIs and develop signatures of response to chemotherapy (SPECS trial). Importantly we propose to develop a unique in depth analysis of the tissue proteome by shotgun analysis, coupled with mass spectrometry-based quantitative analysis of candidate biomarkers in both tissue and serum. These molecular signatures will lead to greater insight into lung tumorigenesis and tumor behavior and improved diagnostic tools to allow earlier and more targeted therapeutic interventions in an attempt to reduce the morbidity and mortality from lung cancer.